Design a test tube ensemble intended to contain a 4-stranded stick figure at 1 M.
Material: RNA
Temperature: 23 C
# Import Python NUPACK module
from nupack import *
# Define physical model
my_model = Model(material='rna', celsius=23)
# Define sequence domains
da = Domain('N27', name='da')
db = Domain('N29', name='db')
dc = Domain('N25', name='dc')
dd = Domain('N18', name='dd')
# Define strands containing these domains
sa = TargetStrand([da], name='sa')
sb = TargetStrand([db], name='sb')
sc = TargetStrand([dc], name='sc')
sd = TargetStrand([dd], name='sd')
# Define a target complex
cstickfigure = TargetComplex([sa, sb, sc, sd], '..((((((((..((((((((((((...+))))))(((.........)))((((((..+.))))))))))))..((((((((..+.)))))))))))))))).', name='cstickfigure')
#Define a target test tube containing all off-target complexes of up to 4 strands
tstickfigure = TargetTube(on_targets={cstickfigure: 1e-06}, off_targets=SetSpec(max_size=4), name='tfigure')
# Set a stop condition of 1% and a seed for random number generation to get a reproducible result for this demo
my_options = DesignOptions(f_stop=0.01, seed=93)
# Define and run the test tube design job
my_design = tube_design(tubes=[tstickfigure], model=my_model, options=my_options)
my_results = my_design.run(trials=1)[0]
# Display the design results
my_results
Domain | Sequence |
---|---|
da | GGGCCACAGCGAUACAGAGCUCCCGAA |
da* | UUCGGGAGCUCUGUAUCGCUGUGGCCC |
db | GGGAGCCGCAAAAACGAAGCGCAGACCAC |
db* | GUGGUCUGCGCUUCGUUUUUGCGGCUCCC |
dc | AGGUCUGUCUGUAAACCAGGAUCGG |
dc* | CCGAUCCUGGUUUACAGACAGACCU |
dd | GGAUCCUGGGCUGUGGCA |
dd* | UGCCACAGCCCAGGAUCC |
Strand | Sequence |
---|---|
sa | GGGCCACAGCGAUACAGAGCUCCCGAA |
sd | GGAUCCUGGGCUGUGGCA |
sb | GGGAGCCGCAAAAACGAAGCGCAGACCAC |
sc | AGGUCUGUCUGUAAACCAGGAUCGG |
Objective type | Value |
---|---|
Weighted ensemble defect | 0.00973 |
Complex | Complex defect (nt) | Normalized complex defect |
---|---|---|
cstickfigure | 0.144 | 0.00145 |
Tube | Tube defect (M) | Normalized tube defect |
---|---|---|
tfigure | 9.63e-07 | 0.00973 |
Tube | On-target complex | Structural defect (M) | Concentration defect (M) | Total defect (M) |
---|---|---|---|---|
tfigure | cstickfigure | 1.43e-07 | 8.20e-07 | 9.63e-07 |
Tube | Complex | Concentration (M) | Target concentration (M) |
---|---|---|---|
tfigure | cstickfigure | 9.92e-07 | 1.00e-06 |
Tube | Complex | Concentration (M) |
---|---|---|
tfigure | — | — |
# For more detail, display the analysis results performed on the designed tube ensemble
my_results.analysis_result
Complex | Pfunc | ΔG (kcal/mol) |
---|---|---|
(sa) | 7.2963e+6 | -9.300 |
(sb) | 1.0985e+5 | -6.831 |
(sc) | 5.3855e+4 | -6.411 |
(sd) | 1.0682e+2 | -2.749 |
(sa+sa) | 1.3227e+17 | -23.201 |
(sa+sb) | 3.5730e+18 | -25.141 |
(sb+sb) | 6.1891e+12 | -17.334 |
(sc+sa) | 1.8364e+15 | -20.684 |
(sc+sb) | 6.6467e+17 | -24.151 |
(sc+sc) | 6.3860e+12 | -17.352 |
(sd+sa) | 1.1953e+22 | -29.917 |
(sd+sb) | 2.0554e+19 | -26.170 |
(sd+sc) | 4.0646e+20 | -27.927 |
(sd+sd) | 1.3046e+14 | -19.127 |
(sa+sa+sa) | 8.0996e+27 | -37.818 |
(sa+sa+sb) | 3.5667e+31 | -42.756 |
(sa+sb+sb) | 9.2621e+27 | -37.897 |
(sb+sb+sb) | 2.1204e+21 | -28.899 |
(sc+sa+sa) | 3.7186e+27 | -37.360 |
(sc+sa+sb) | 1.1711e+33 | -44.810 |
(sc+sb+sa) | 3.4134e+25 | -34.599 |
(sc+sb+sb) | 6.8483e+26 | -36.364 |
(sc+sc+sa) | 1.8138e+25 | -34.227 |
(sc+sc+sb) | 1.8165e+27 | -36.938 |
(sc+sc+sc) | 1.5174e+21 | -28.702 |
(sd+sa+sa) | 8.1024e+31 | -43.238 |
(sd+sa+sb) | 9.4843e+35 | -48.751 |
(sd+sa+sc) | 1.2360e+36 | -48.907 |
(sd+sb+sa) | 8.7833e+29 | -40.576 |
(sd+sb+sb) | 7.3575e+27 | -37.761 |
(sd+sb+sc) | 3.7580e+34 | -46.852 |
(sd+sc+sa) | 2.0259e+28 | -38.358 |
(sd+sc+sb) | 1.0165e+27 | -36.597 |
(sd+sc+sc) | 9.2618e+29 | -40.607 |
(sd+sd+sa) | 5.8774e+31 | -43.050 |
(sd+sd+sb) | 5.3791e+28 | -38.932 |
(sd+sd+sc) | 6.7221e+28 | -39.063 |
(sd+sd+sd) | 2.2617e+24 | -33.002 |
cstickfigure | 5.0030e+54 | -74.121 |
(sa+sa+sa+sa) | 4.9539e+39 | -53.790 |
(sa+sa+sa+sb) | 2.7586e+42 | -57.510 |
(sa+sa+sb+sb) | 2.4526e+41 | -56.086 |
(sa+sb+sa+sb) | 6.0933e+44 | -60.687 |
(sa+sb+sb+sb) | 7.3189e+37 | -51.309 |
(sb+sb+sb+sb) | 1.6566e+31 | -42.304 |
(sc+sa+sa+sa) | 3.4036e+39 | -53.569 |
(sc+sa+sa+sb) | 1.5398e+46 | -62.587 |
(sc+sa+sb+sa) | 2.7859e+41 | -56.161 |
(sc+sa+sb+sb) | 2.5443e+43 | -58.818 |
(sc+sa+sc+sa) | 8.1008e+36 | -50.014 |
(sc+sb+sa+sa) | 1.5895e+37 | -50.410 |
(sc+sb+sa+sb) | 1.1887e+42 | -57.015 |
(sc+sb+sb+sa) | 5.6597e+36 | -49.803 |
(sc+sb+sb+sb) | 3.9540e+36 | -49.592 |
(sc+sb+sc+sa) | 2.2230e+39 | -53.318 |
(sc+sb+sc+sb) | 8.6883e+40 | -55.475 |
(sc+sc+sa+sa) | 2.7228e+37 | -50.727 |
(sc+sc+sa+sb) | 5.1991e+43 | -59.238 |
(sc+sc+sb+sa) | 3.2206e+35 | -48.116 |
(sc+sc+sb+sb) | 2.0476e+37 | -50.559 |
(sc+sc+sc+sa) | 7.4614e+34 | -47.255 |
(sc+sc+sc+sb) | 2.8406e+36 | -49.397 |
(sc+sc+sc+sc) | 1.3147e+30 | -40.813 |
(sd+sa+sa+sa) | 7.0757e+44 | -60.775 |
(sd+sa+sa+sb) | 6.7866e+45 | -62.105 |
(sd+sa+sa+sc) | 1.6608e+48 | -65.342 |
(sd+sa+sb+sa) | 1.9106e+46 | -62.714 |
(sd+sa+sb+sb) | 7.7559e+45 | -62.184 |
(sd+sa+sc+sa) | 5.9960e+43 | -59.322 |
(sd+sa+sc+sb) | 3.3892e+42 | -57.631 |
(sd+sa+sc+sc) | 8.3391e+46 | -63.582 |
(sd+sa+sd+sa) | 4.4940e+48 | -65.928 |
(sd+sb+sa+sa) | 2.7919e+40 | -54.807 |
(sd+sb+sa+sb) | 7.9413e+43 | -59.488 |
(sd+sb+sa+sc) | 9.4562e+43 | -59.590 |
(sd+sb+sb+sa) | 1.1982e+39 | -52.954 |
(sd+sb+sb+sb) | 8.6729e+36 | -50.054 |
(sd+sb+sb+sc) | 8.3313e+44 | -60.871 |
(sd+sb+sc+sa) | 4.8736e+42 | -57.845 |
(sd+sb+sc+sb) | 1.4393e+41 | -55.772 |
(sd+sb+sc+sc) | 7.8085e+44 | -60.833 |
(sd+sb+sd+sa) | 4.5687e+45 | -61.872 |
(sd+sb+sd+sb) | 1.3624e+42 | -57.095 |
(sd+sb+sd+sc) | 1.8854e+43 | -58.641 |
(sd+sc+sa+sa) | 7.2662e+41 | -56.725 |
(sd+sc+sa+sb) | 1.9599e+42 | -57.309 |
(sd+sc+sa+sc) | 4.6842e+41 | -56.467 |
(sd+sc+sb+sa) | 1.9310e+40 | -54.590 |
(sd+sc+sb+sb) | 5.8112e+37 | -51.173 |
(sd+sc+sb+sc) | 7.2097e+42 | -58.076 |
(sd+sc+sc+sa) | 1.2886e+39 | -52.997 |
(sd+sc+sc+sb) | 6.3004e+38 | -52.576 |
(sd+sc+sc+sc) | 6.6791e+38 | -52.610 |
(sd+sc+sd+sa) | 3.7955e+47 | -64.473 |
(sd+sc+sd+sc) | 1.5972e+45 | -61.254 |
(sd+sd+sa+sa) | 7.8733e+46 | -63.548 |
(sd+sd+sa+sb) | 3.3319e+48 | -65.752 |
(sd+sd+sa+sc) | 6.1991e+47 | -64.762 |
(sd+sd+sb+sa) | 1.1258e+44 | -59.693 |
(sd+sd+sb+sb) | 4.3339e+41 | -56.421 |
(sd+sd+sb+sc) | 1.5714e+45 | -61.244 |
(sd+sd+sc+sa) | 4.7031e+41 | -56.469 |
(sd+sd+sc+sb) | 1.1504e+39 | -52.930 |
(sd+sd+sc+sc) | 5.0363e+42 | -57.864 |
(sd+sd+sd+sa) | 2.4808e+44 | -60.158 |
(sd+sd+sd+sb) | 2.9435e+39 | -53.483 |
(sd+sd+sd+sc) | 2.7524e+41 | -56.154 |
(sd+sd+sd+sd) | 1.5291e+37 | -50.388 |
Complex | tfigure (M) | |
---|---|---|
cstickfigure | 9.917e-07 | |
(sb) | 7.188e-09 | |
(sa) | 5.666e-09 | |
(sd+sc) | 4.821e-09 | |
(sc) | 2.691e-09 | |
(sd+sa) | 2.203e-09 | |
(sd+sb+sc) | 5.289e-10 | |
(sd+sb) | 3.192e-10 | |
(sd+sa+sb) | 2.074e-10 | |
(sd+sa+sc) | 2.065e-10 | |
(sc+sb) | 3.941e-11 | |
(sa+sb) | 3.293e-12 | |
(sd) | 1.398e-12 | |
(sc+sa+sb) | 9.780e-13 | |
(sd+sd+sa+sb) | 1.730e-13 | |
(sd+sd+sa+sc) | 2.458e-14 | |
(sd+sc+sd+sa) | 1.505e-14 | |
(sd+sb+sb+sc) | 1.391e-14 | |
(sd+sa+sc+sc) | 1.262e-14 | |
(sd+sb+sc+sc) | 9.960e-15 | |
(sd+sc+sc) | 9.955e-15 | |
(sd+sc+sd+sc) | 8.149e-15 | |
(sd+sa+sd+sa) | 5.538e-15 | |
(sd+sd+sb+sc) | 5.249e-15 | |
(sd+sa+sa+sc) | 3.907e-15 | |
(sa+sa) | 2.893e-15 | |
(sd+sd+sa) | 2.571e-15 | |
(sd+sa+sb+sb) | 2.013e-15 | |
(sc+sa) | 1.292e-15 | |
(sb+sb) | 9.612e-16 | |
(sd+sd) | 8.104e-16 | |
(sc+sc) | 5.784e-16 | |
(sa+sa+sb) | 4.629e-16 | |
(sd+sb+sd+sa) | 2.372e-16 | |
(sd+sa+sa) | 2.103e-16 | |
(sd+sd+sb) | 1.983e-16 | |
(sd+sb+sa) | 1.921e-16 | |
(sd+sd+sc) | 1.892e-16 | |
(sc+sa+sa+sb) | 1.811e-16 | |
(sd+sb+sb) | 1.356e-16 | |
(sc+sc+sb) | 9.762e-17 | |
(sd+sc+sb+sc) | 9.196e-17 | |
(sd+sb+sd+sc) | 6.298e-17 | |
(sd+sa+sb+sa) | 5.886e-17 | |
(sd+sd+sa+sa) | 4.851e-17 | |
(sc+sb+sb) | 4.819e-17 | |
(sc+sc+sa+sb) | 3.935e-17 | |
(sc+sa+sb+sb) | 2.522e-17 | |
(sd+sa+sa+sb) | 2.091e-17 | |
(sd+sb+sa+sb) | 2.061e-17 | |
(sa+sb+sa+sb) | 1.877e-17 | |
(sd+sb+sa+sc) | 1.874e-17 | |
(sd+sc+sb) | 1.431e-17 | |
(sd+sd+sc+sc) | 1.285e-17 | |
(sd+sb+sd+sb) | 1.192e-17 | |
(sc+sb+sc+sb) | 1.108e-17 | |
(sa+sb+sb) | 1.013e-17 | |
(sd+sd+sb+sa) | 5.844e-18 | |
(sd+sc+sa) | 3.384e-18 | |
(sd+sd+sd+sa) | 2.576e-18 | |
(sd+sb+sc+sb) | 2.404e-18 | |
(sd+sd+sb+sb) | 1.896e-18 | |
(sc+sb+sa+sb) | 1.178e-18 | |
(sd+sb+sc+sa) | 9.661e-19 | |
(sd+sa+sc+sb) | 6.718e-19 | |
(sd+sc+sa+sb) | 3.885e-19 | |
(sd+sd+sd+sc) | 1.839e-19 | |
(sd+sa+sc+sa) | 1.411e-19 | |
(sd+sc+sa+sc) | 7.091e-20 | |
(sc+sa+sa) | 3.686e-20 | |
(sc+sb+sa) | 2.851e-20 | |
(sd+sa+sa+sa) | 2.587e-20 | |
(sd+sd+sc+sa) | 1.865e-20 | |
(sc+sc+sa) | 1.157e-20 | |
(sd+sc+sc+sb) | 8.036e-21 | |
(sd+sc+sc+sc) | 6.506e-21 | |
(sd+sd+sd) | 5.002e-21 | |
(sd+sd+sc+sb) | 3.843e-21 | |
(sd+sc+sb+sa) | 3.828e-21 | |
(sa+sa+sb+sb) | 3.778e-21 | |
(sa+sa+sa) | 3.743e-21 | |
(sc+sa+sb+sa) | 3.277e-21 | |
(sd+sd+sd+sb) | 2.575e-21 | |
(sd+sc+sa+sa) | 1.709e-21 | |
(sc+sb+sc+sa) | 1.683e-21 | |
(sc+sc+sb+sb) | 1.306e-21 | |
(sd+sc+sb+sb) | 9.706e-22 | |
(sb+sb+sb) | 5.862e-22 | |
(sa+sa+sa+sb) | 5.043e-22 | |
(sc+sb+sb+sb) | 3.302e-22 | |
(sd+sb+sb+sa) | 3.110e-22 | |
(sd+sc+sc+sa) | 1.951e-22 | |
(sd+sb+sb+sb) | 1.897e-22 | |
(sc+sc+sc) | 1.868e-22 | |
(sc+sc+sc+sb) | 1.383e-22 | |
(sa+sb+sb+sb) | 9.498e-23 | |
(sd+sb+sa+sa) | 8.601e-23 | |
(sd+sd+sd+sd) | 1.070e-23 | |
(sc+sb+sb+sa) | 5.609e-24 | |
(sc+sa+sa+sa) | 4.751e-25 | |
(sc+sc+sa+sa) | 2.446e-25 | |
(sc+sc+sb+sa) | 2.438e-25 | |
(sc+sb+sa+sa) | 1.870e-25 | |
(sc+sa+sc+sa) | 1.455e-25 | |
(sc+sc+sc+sa) | 4.313e-26 | |
(sa+sa+sa+sa) | 4.299e-26 | |
(sb+sb+sb+sb) | 7.246e-27 | |
(sc+sc+sc+sc) | 1.956e-28 |